1: Annotation of Wilms Dataset

There were 72501 cells passing the quality control in the article, and 11407 of them were sampled from wilms patients. It will be included in this analysis if the cell passed the QC and were from wilms patients.

The first round of annotation followed the pipeline as “clustering –> finding differentially expressed gene –> manual annotation”. As the author instructed, the batch effect between different 10X channels was removed via “harmony”.

distribution of canonical marker
differentially expressed genes in each seurat_cluster
Annotation from the author

2: Annotation of T cell in Wilms Dataset

2.1: Manual Annotation

The ratio of CD4/CD8 Tcell based on manual annotation is (batch effect has been removed):
Wilms1: 1.3560606
Wilms2: 0.1666667
Wilms3: 2.5378151

UMAP plot with batch effect removed
distribution of canonical marker
differentially expressed genes in each seurat_cluster

2.2: SingleR Annotation

The ratio of CD4/CD8 Tcell based on SingleR annotation is :
Wilms1: 3.7346939
Wilms2: 0.75
Wilms3: 15.5384615

2.3: Annotation from raw article

The ratio is calculated as the sum of T regulatory and Th cell divide by the count of CD8 T cell.
Wilms1: 0.8969072
Wilms2: 4.5
Wilms3: 5.9310345